[med-svn] samtools 02/02: Refreshed to for upstream version 1.0.

[Charles Plessy]

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plessy pushed a commit to branch debian/unstable
in repository samtools.

commit d062687c6fed2a74712a9ea426335781f351efbc
Author: Charles Plessy <plessy at debian.org>
Date:   Fri Aug 22 07:53:22 2014 +0900

    Refreshed to for upstream version 1.0.
---
 debian/patches/fix_segfault_with_small_ref.patch | 96 ++++++++++++------------
 1 file changed, 47 insertions(+), 49 deletions(-)

diff --git a/debian/patches/fix_segfault_with_small_ref.patch b/debian/patches/fix_segfault_with_small_ref.patch
index 0f1f665..00f7f75 100644
--- a/debian/patches/fix_segfault_with_small_ref.patch
+++ b/debian/patches/fix_segfault_with_small_ref.patch
@@ -1,53 +1,51 @@
 Description: Fix segfault if position is outside of the reference sequence length
 Origin: Don Armstrong <don at donarmstrong.com>
 
-Index: samtools/bam_plcmd.c
-===================================================================
---- samtools.orig/bam_plcmd.c
-+++ samtools/bam_plcmd.c
-@@ -96,6 +96,7 @@
- 	bam_iter_t iter;
- 	bam_header_t *h;
- 	int ref_id;
-+        int ref_len;
- 	char *ref;
- 	const mplp_conf_t *conf;
+--- a/bam_plcmd.c
++++ b/bam_plcmd.c
+@@ -127,6 +127,7 @@
+     hts_itr_t *iter;
+     bam_hdr_t *h;
+     int ref_id;
++    int ref_len;
+     char *ref;
+     const mplp_conf_t *conf;
  } mplp_aux_t;
-@@ -139,6 +140,11 @@
- 				qual[i] = qual[i] > 31? qual[i] - 31 : 0;
- 		}
- 		has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
-+		if (has_ref && (ma->ref_len <= b->core.pos)) { // exclude reads outside of the reference sequence
-+		  fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n",__func__,b->core.pos,ma->ref_len,ma->ref_id);
-+		  skip = 1;
-+		  continue;
-+		}
- 		skip = 0;
- 		if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
- 		if (has_ref && ma->conf->capQ_thres > 10) {
-@@ -307,7 +313,11 @@
- 	if (tid0 >= 0 && conf->fai) { // region is set
- 		ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
- 		ref_tid = tid0;
--		for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
-+		for (i = 0; i < n; ++i) {
-+		  data[i]->ref = ref;
-+                  data[i]->ref_id = tid0;
-+		  data[i]->ref_len = ref_len;
-+                }
- 	} else ref_tid = -1, ref = 0;
- 	iter = bam_mplp_init(n, mplp_func, (void**)data);
- 	max_depth = conf->max_depth;
-@@ -325,7 +335,11 @@
- 		if (tid != ref_tid) {
- 			free(ref); ref = 0;
- 			if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
--			for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
-+			for (i = 0; i < n; ++i) {
-+			  data[i]->ref = ref;
-+			  data[i]->ref_id = tid;
-+			  data[i]->ref_len = ref_len;
-+			}
- 			ref_tid = tid;
- 		}
- 		if (conf->flag & MPLP_GLF) {
+@@ -172,6 +173,11 @@
+                 qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+         }
+         has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
++        if (has_ref && (ma->ref_len <= b->core.pos)) { // exclude reads outside of the reference sequence
++            fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n",__func__,b->core.pos,ma->ref_len,ma->ref_id);
++            skip = 1;
++            continue;
++        }
+         skip = 0;
+         if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
+         if (has_ref && ma->conf->capQ_thres > 10) {
+@@ -419,7 +425,11 @@
+     if (tid0 >= 0 && conf->fai) { // region is set
+         ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len);
+         ref_tid = tid0;
+-        for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0;
++        for (i = 0; i < n; ++i) {
++            data[i]->ref = ref;
++            data[i]->ref_id = tid0;
++            data[i]->ref_len = ref_len;
++        }
+     } else ref_tid = -1, ref = 0;
+ 
+     // begin pileup
+@@ -442,7 +452,11 @@
+         if (tid != ref_tid) {
+             free(ref); ref = 0;
+             if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len);
+-            for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid;
++            for (i = 0; i < n; ++i) {
++                data[i]->ref = ref;
++                data[i]->ref_id = tid;
++                data[i]->ref_len = ref_len;
++            }
+             ref_tid = tid;
+         }
+         if (conf->flag & MPLP_BCF) {

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